title: A4_SHH
description: Protocols: Brain organoids were harvested on day 19 to perform 10x multiome scRNA- and scATAC-seq. Single cell suspensions were acquired by dissociation of the organoids with a papain-based dissociation (Miltenyi Biotec, 130-092-628). The induced pluripotent stem cell line 409B2 was used for this experiment. The wild type GLI3-mediated cell line with inducible Cas9 nickase were generated through editing process. GLI3 WT cerebral organoids were generated using the protocol by Lancaster 2014 (https://doi.org/10.1038/nprot.2014.158 ), and were treated with or without 200 ng/mL Sonic Hedgehog (SHH, R&D systems, 1845-SH-025/CF) daily starting three days prior to the experiment on day 19. After dissociation, cell viability was checked, cells were counted and 7000 cells were targeted per lane of the 10x microfluidic chip. Combined scRNA-seq and scATAC-seq were generated with the Chromium Single Cell Multiome ATAC + Gene Expression kit.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2022-09-01
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2022-09-01
attributes.tag: External Id
attributes.value: SAMEA110684776
attributes.tag: INSDC center alias
attributes.value: ETH Zurich, DBSSE
attributes.tag: INSDC center name
attributes.value: ETH Zurich, DBSSE
attributes.tag: INSDC first public
attributes.value: 2022-09-01T00:14:27Z
attributes.tag: INSDC last update
attributes.value: 2022-09-01T00:14:27Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-12003:A4_SHH
attributes.tag: age
attributes.value: 36
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: 409B2
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: normal
attributes.tag: genotype
attributes.value: inducible Cas9 nickase
attributes.tag: growth condition
attributes.value: cerebral organoid culture
attributes.tag: organism part
attributes.value: dermis
attributes.tag: progenitor cell type
attributes.value: induced pluripotent stem cell
attributes.tag: sample name
attributes.value: E-MTAB-12003:A4_SHH
attributes.tag: sex
attributes.value: female